Is it in an area with gradients at all? sounds like an id clash between the gradients in the different files meaning the wrong ones getting referenced.

2008/7/10 Quentin Hartman <qhartman@gmail.com>:
I often use Inkscape to build network diagrams. I've collected a
number of SVG images (mostly from Tango Icons) which I use as objects
in those diagrams. On my Ubuntu Hardy box today I discovered that once
I get a number of objects into a document, if I import a single new
object, the colors on it get all messed up upon import. This never
happened before. Opening the object alone, or importing it into a new
document works fine. Have any of you seen this behavior in .46? If so,
have you figured out a work-around? Might it have something to do with
the (new?) color management stuff?  I chose not to attach files to the
list because they are rather large, but I would be happy to send
examples to anyone interested in exploring this off-list.

--
-Regards-

-Quentin Hartman-

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